Dannon Baker
39eb262219
More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16
2016-02-02 13:54:24 -05:00
Dannon Baker
ba9ad97c40
Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details.
2016-02-02 09:30:30 -05:00
John Chilton
61fda5f23d
Add missing file from previous commit.
2015-09-23 15:10:06 +01:00
John Chilton
2b02677e85
Workaround for metadata_bam.xml failure.
2015-09-19 10:27:09 +01:00
anton
41343e4b41
Added test for bcf index creation.
2015-04-28 13:45:33 -04:00
John Chilton
3fc5325d52
Remove test data files only used by tool tests.
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These files are being moved to https://github.com/galaxyproject/galaxy-test-data .
Files used by framework functional tests remain. This drops the size of the test-data directory from 73M down to less than 1.3M.
2015-02-09 21:43:57 -05:00
John Chilton
3688e02475
Add framework test tool that has both data and data_collection param - with test case.
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Tool test is mildly useful to verify this works for single execution - but more useful as basis for future changesets testing mixed collection and subcollection mapping tool executions.
2014-05-07 15:39:03 -05:00
Dave Bouvier
424efdcf9a
Moved API tests to live under test/ rather than test/functional/. Removed test for DNAse flanked genes. Added test for UCSC table browser.
2014-04-30 15:35:57 -04:00
John Chilton
3ac17e09f1
Rework test framework testing and tools.
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-framework will still cause just a small set of non-default, non-user facing tools to be tested and exerise various aspects of the tool and test frameworks, but now an argument can be passed in -with_framework_test_tools to allow these tools to be used as part of the normal test framework (i.e. when not using -framework). This serves two purposes - to ensure the feature coverage of existing tests remains high as the tests are migrated out of the distribution and to allow a set of tests to be available for functional (e.g. API tests) that users don't need to see.
2014-04-28 11:48:51 -05:00
Dave Bouvier
da74f1ea78
Fix library security functional tests.
2014-04-25 15:29:56 -04:00
Dave Bouvier
ac68f98bbd
Fix certain failing functional tests.
2014-04-16 16:13:11 -04:00
Dave Bouvier
83af05b1f2
Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
2014-04-01 11:04:32 -04:00
Dave Bouvier
448d9f55eb
Migrate 43 tools from the distribution to the tool shed.
2014-01-27 09:53:14 -05:00
Dave Bouvier
9402faf4fc
Remove files from test-data that are not referenced in any tool test definition or functional test script.
2014-01-08 14:15:53 -05:00
Dave Bouvier
bb25625d31
Restore files that were deleted due to a tool migration, but are still used in test/functiona/test_get_data.py.
2013-11-13 10:46:38 -05:00
Ross Lazarus
c860c25f77
Remove unused test-data/rtestouts
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Remove references in converters to g2.bx.psu.edu
Note leaving rgenetics converters and datatypes - ped still used in genomic variation tools.
2013-10-14 21:43:32 +11:00
Dave Bouvier
b0efe4ddea
Migrate tools from the distribution to the tool shed, including but not limited to samtools and fastx_toolkit tools.
2013-09-26 10:05:00 -04:00
Jeremy Goecks
ea8d337316
Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.
2013-01-29 10:37:16 -05:00
Jeremy Goecks
9719bed6f9
Enable BedGraph to be used as input to wig-to-bigwig tool.
2013-01-24 17:06:51 -05:00
Dannon Baker
0b2e939d4d
Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.
2012-08-22 16:12:59 -04:00
Greg Von Kuster
fb1f65a057
Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed.
2012-03-21 16:41:45 -04:00
Kanwei Li
c0a1b39214
Add missing test files
2011-06-10 20:10:09 -04:00
Kanwei Li
34155271b3
[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537 . Fixes #535
2011-05-27 10:47:17 +02:00
Ross Lazarus
7859f56954
reverting reorder test outputs - PhiX reference used to generate them seems different from that on the buildbot
2011-05-13 21:24:03 -04:00
Ross Lazarus
5e25812f6f
finally have picard reorder tests working
2011-05-13 17:12:19 -04:00
Kanwei Li
af3f4a2ff9
More BLAST tests
2011-04-06 12:38:00 -04:00
Nate Coraor
d765f607c4
Slight output difference on the buildbot for weblogo, hopefully the difference is static.
2011-03-23 16:42:14 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Ross Lazarus
6646cfa80d
Adding two new tool wrappers and tests - clustalw ( http://www.clustal.org ) for multiple alignments and a sequence motif generator based on weblogo3 ( http://weblogo.berkeley.edu ) which works on fasta files such as alignments from clustalw
2011-03-22 14:08:32 -04:00
Nate Coraor
ea0e8ead22
Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully
2011-03-02 13:46:07 -05:00
Kelly Vincent
7d0ff14df9
Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.
2010-11-08 00:10:13 -05:00
Jeremy Goecks
ccf07c72aa
Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.
2010-11-04 16:30:34 -04:00
Nate Coraor
dd09a19fc2
Updated test outputs for pdf/image output tools that differ slightly on updated dependencies.
2010-09-29 17:25:31 -04:00
Nate Coraor
8e05ce7817
Add test for bz2 file upload
2010-09-10 14:17:05 -04:00
Kelly Vincent
3b12bb72e9
Fixing buildbot tests: added missing column join test files; regenerated and enhanced BWA test files; sorted tophat_out1.sam and specified sort=True in test for it
2010-08-25 21:51:41 -04:00
Greg Von Kuster
a7e30c4441
Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.
2010-08-19 13:58:10 -04:00
Nate Coraor
6e7427e8e2
Removed binseq.zip test and replace it with a zip test.
2010-07-01 08:59:26 -04:00
Jeremy Goecks
eed5d297c3
Add GFF support to GOPS subtract tool and updated functional tests. Using the GFF-->BED converter is lossy as GFF has more attributes/features than BED, so it's necessary to directly support GFF. Basic approach used is to modify interval coordinates during reading and writing while not changing the middle, computational steps; this approach can be used to provide GFF support for any tool that uses bx-python to operate on intervals.
2010-06-07 16:28:46 -04:00
Daniel Blankenberg
183c2d3d13
Bug fix for handling 'spaces to tab' for non-binary composite datatype files.
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Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes.
2010-06-07 15:34:20 -04:00
Ross Lazarus
aae3898b4f
Adding rg test outputs and updated tools
2010-03-26 14:42:15 -04:00
Kelly Vincent
710e9cfd07
Added new tabular/pileup join tool and associated test files. Also added pileup datatype.
2010-03-26 12:00:55 -04:00
Kelly Vincent
09fa3f0bf1
Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools.
2010-02-24 07:11:43 -05:00
Daniel Blankenberg
8082c6f36f
Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid.
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Tools include:
FASTQ Groomer convert between various FASTQ quality formats
Combine FASTA and QUAL into FASTQ
FASTQ joiner on paired end reads
FASTQ splitter on joined paired end reads
FASTQ to FASTA converter
FASTQ Summary Statistics by column
Filter FASTQ reads by quality score and length
FASTQ Trimmer by column
Manipulate FASTQ reads on various attributes
Boxplot of quality statistics (Generic, with outliers)
2010-02-23 16:48:07 -05:00
Greg Von Kuster
72e7836cbb
Enhance functional test framework so that a boolean form field ( checkbox ) can have a false value ( be unchecked ). Add a 2nd test to gops_concat that uses this behavior.
2010-02-17 11:07:08 -05:00
Guruprasad Anada
fb9147e83d
Fixed functional tests for short_reads_figure_score tool.
2010-01-08 11:28:37 -05:00
Greg Von Kuster
aa36d79d30
Update the output datasets for functional test for the quality_score_distribution tool due to a new version of R - update tool version as well.
2009-12-10 10:56:01 -05:00
Greg Von Kuster
bcd6751cdf
Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.
2009-12-07 16:04:33 -05:00
Daniel Blankenberg
f92b25d2f5
Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .
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Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles.
Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes.
Future Enhancement:
Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
2009-12-07 10:19:41 -05:00
Greg Von Kuster
08e0d5e532
Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.
2009-12-04 19:51:46 -05:00
Greg Von Kuster
0e807f13f5
Add support for uploading BAM files.
2009-12-02 20:02:05 -05:00
Dannon Baker